Install ShuTu on Colab
The goal of this notebook is simply to install ShuTu SWC generator on Colab. The ShuTu SWC editor desktop app is out of scope.
This install script is based on the ShuTu tutorial but things are tweaked and tuned for installation on Colab. (The default instructions raise a harmless but confusing error on Colab.) See test_install_of_shutu_on_colab.ipynb, for a blow-by-blow log of how this script was developed for deploying ShuTu, but specifically on Colab.
ShuTu only needs to be installed once per VM run (max of 12 hours) so it is useful to have installation be a separate notebook.
ShuTu can be installed using the default method as run through in brightfield_neuron_swc_by_shutu_on_colab.ipynb. It works but generates a harmless error at the end of build.sh. So instead, here the core of build.sh is recreated as a Colab code cell. For an explanation see GitHub Issues. Basically, the build.sh boils down to calling make twice in the appropriate directories.
!pwd
!ls -l
/content total 4 drwxr-xr-x 1 root root 4096 Aug 27 16:17 sample_data
%%shell
# Get the Linux distro of ShuTu (took less than a minute to DL)
wget https://psu.box.com/shared/static/wszpq3r6hwgoxo8eq0vb1k82fwrabycl.zip
unzip wszpq3r6hwgoxo8eq0vb1k82fwrabycl.zip # creates ShuTuUbuntu directory
#set -m # needed to avoid error: bash: no job control in this shell
cd ShuTuUbuntu
##########
# This next part is from build.sh.
#
#export PATH=$downloadDir/local/bin:$PATH
cd mylib
make
cd ..
make
--2019-10-14 00:13:02-- https://psu.box.com/shared/static/wszpq3r6hwgoxo8eq0vb1k82fwrabycl.zip Resolving psu.box.com (psu.box.com)... 185.235.236.197 Connecting to psu.box.com (psu.box.com)|185.235.236.197|:443... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: /public/static/wszpq3r6hwgoxo8eq0vb1k82fwrabycl.zip [following] --2019-10-14 00:13:02-- https://psu.box.com/public/static/wszpq3r6hwgoxo8eq0vb1k82fwrabycl.zip Reusing existing connection to psu.box.com:443. HTTP request sent, awaiting response... 301 Moved Permanently Location: https://psu.app.box.com/public/static/wszpq3r6hwgoxo8eq0vb1k82fwrabycl.zip [following] --2019-10-14 00:13:02-- https://psu.app.box.com/public/static/wszpq3r6hwgoxo8eq0vb1k82fwrabycl.zip Resolving psu.app.box.com (psu.app.box.com)... 185.235.236.199 Connecting to psu.app.box.com (psu.app.box.com)|185.235.236.199|:443... connected. HTTP request sent, awaiting response... 302 Found Location: https://public.boxcloud.com/d/1/b1!Wwkmy831DjvbaLlQhmhSp-BTmAUE-G3oAZWwzc5BXSLI90-cQu4n7qjUPoGip6hwOwyRE7ktDB34rD7vLsgPQAXJda8vYe6LKds3RvWyBmhpKknYueTppKSU6GWz6UGj7wyJPxSyxi0sTiP5AHzEuf5MDFWEX9ZnUH5JqSzgHlRre_5y6rufEjFNNyV3JgpAgf2apJ8DB-0cKTgjeZs9OP5Bqyqo0GXNUC9TZrAN4pnGtWIGkAZIMbu3PzI7gvH24mxBf5L91u8UksNoJS8H4WiYQZ9PC_xEo8JYcaW2RB33XCzISYkFk7kHua4ckOZvZE5GjOBXEanHeB480mi5FKYDCsMyZ1Q0clVnf3AdzMS7lMNjK0xCscAxo-C48tNsQNOdlp5y7Y5e6vUjS703rma5c7k2TsDaDsZQupszm_lL9v6UhzuRPnlogIW-ESBJAmsSNX-JjNYLSSvXHh7djpH2n_l7urp1xTWIHQR9n2W29yH6rf4PTxW6JkddrPgPTiTEqvhTLbbDiTqtahH1A04oDcknmv77YlFYIJe-c6zuCMge643-9RsIoYh8xCTSmBRN1heJW3Zrm5kKgUcwmlGDqinmI3AfP7l9h9EnyCowBt4pBzLYu8eAHb_FfNyN1TMnLhjs-VkpNigABwXLJ8QCFjm-qyzV5QlcRXB9O6zptRQ1cHy093tO1P3-Uq-FQrKbEWGnI9rmja24orhvsj2UsZqfpUA5j8y-taxG__EDh9AP_1ahIRjuw9EEqmTT8Stvxq6yYPVmUKxdTT2gTAprYw99nwEgVL-h53soXXiha31-Md8knp9vHHM01P-WQbsuE2LXb1uJUbHGmzPtjo_HEbVOaH0Y4I_9WTGUAVjlJfcbkUAowPY6K3pcxbRDDdBOnhw5yCGKfK3Fmk8jnUdFFMoX0-0zDkC1GiqXdGb38zlxAIMtovIrmJnIYuCGIaV5B1CTjnpIAuqp0Pku4mHUhrm0lKywM0neqmMFjb5FK3cIqTCHO4JVmTPUuxgI7rh9409za24QinO-lfYcthYlF8JRub8nzDURqhbE0FzjzALrPnSnva96ILFlagYqDvqCCAlc1WrR2vtahQdYXNHPrZ6MDM_qjl7p50h8V4FNvumOi6Va8n7haK7l4fTtvz2c1f-thab3nruRvFpgF_cdFwHAdLzKV9i3risc8puqOhgUrbcG6-iHNGeVzhO36nuvV4AIEmA9xO4V3g11bCRQBtilGnOYRfzueiQGW7TK8FqScZ09wL4_TKRsFBUNQ3Jt0dKe22oCtSxdIcS0C6hm2haApGCVpGJ9K6nJzeukDAOfHmFEZObrRWDSFR65m6kdhw61u8QkHri4wQkAR_7oWave2puhpZlfhjPkca_UfYnc0Ao./download [following] --2019-10-14 00:13:03-- https://public.boxcloud.com/d/1/b1!Wwkmy831DjvbaLlQhmhSp-BTmAUE-G3oAZWwzc5BXSLI90-cQu4n7qjUPoGip6hwOwyRE7ktDB34rD7vLsgPQAXJda8vYe6LKds3RvWyBmhpKknYueTppKSU6GWz6UGj7wyJPxSyxi0sTiP5AHzEuf5MDFWEX9ZnUH5JqSzgHlRre_5y6rufEjFNNyV3JgpAgf2apJ8DB-0cKTgjeZs9OP5Bqyqo0GXNUC9TZrAN4pnGtWIGkAZIMbu3PzI7gvH24mxBf5L91u8UksNoJS8H4WiYQZ9PC_xEo8JYcaW2RB33XCzISYkFk7kHua4ckOZvZE5GjOBXEanHeB480mi5FKYDCsMyZ1Q0clVnf3AdzMS7lMNjK0xCscAxo-C48tNsQNOdlp5y7Y5e6vUjS703rma5c7k2TsDaDsZQupszm_lL9v6UhzuRPnlogIW-ESBJAmsSNX-JjNYLSSvXHh7djpH2n_l7urp1xTWIHQR9n2W29yH6rf4PTxW6JkddrPgPTiTEqvhTLbbDiTqtahH1A04oDcknmv77YlFYIJe-c6zuCMge643-9RsIoYh8xCTSmBRN1heJW3Zrm5kKgUcwmlGDqinmI3AfP7l9h9EnyCowBt4pBzLYu8eAHb_FfNyN1TMnLhjs-VkpNigABwXLJ8QCFjm-qyzV5QlcRXB9O6zptRQ1cHy093tO1P3-Uq-FQrKbEWGnI9rmja24orhvsj2UsZqfpUA5j8y-taxG__EDh9AP_1ahIRjuw9EEqmTT8Stvxq6yYPVmUKxdTT2gTAprYw99nwEgVL-h53soXXiha31-Md8knp9vHHM01P-WQbsuE2LXb1uJUbHGmzPtjo_HEbVOaH0Y4I_9WTGUAVjlJfcbkUAowPY6K3pcxbRDDdBOnhw5yCGKfK3Fmk8jnUdFFMoX0-0zDkC1GiqXdGb38zlxAIMtovIrmJnIYuCGIaV5B1CTjnpIAuqp0Pku4mHUhrm0lKywM0neqmMFjb5FK3cIqTCHO4JVmTPUuxgI7rh9409za24QinO-lfYcthYlF8JRub8nzDURqhbE0FzjzALrPnSnva96ILFlagYqDvqCCAlc1WrR2vtahQdYXNHPrZ6MDM_qjl7p50h8V4FNvumOi6Va8n7haK7l4fTtvz2c1f-thab3nruRvFpgF_cdFwHAdLzKV9i3risc8puqOhgUrbcG6-iHNGeVzhO36nuvV4AIEmA9xO4V3g11bCRQBtilGnOYRfzueiQGW7TK8FqScZ09wL4_TKRsFBUNQ3Jt0dKe22oCtSxdIcS0C6hm2haApGCVpGJ9K6nJzeukDAOfHmFEZObrRWDSFR65m6kdhw61u8QkHri4wQkAR_7oWave2puhpZlfhjPkca_UfYnc0Ao./download Resolving public.boxcloud.com (public.boxcloud.com)... 185.235.236.200 Connecting to public.boxcloud.com (public.boxcloud.com)|185.235.236.200|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 295628950 (282M) [application/zip] Saving to: ‘wszpq3r6hwgoxo8eq0vb1k82fwrabycl.zip’ wszpq3r6hwgoxo8eq0v 100%[===================>] 281.93M 12.1MB/s in 25s 2019-10-14 00:13:28 (11.4 MB/s) - ‘wszpq3r6hwgoxo8eq0vb1k82fwrabycl.zip’ saved [295628950/295628950] Archive: wszpq3r6hwgoxo8eq0vb1k82fwrabycl.zip creating: ShuTuUbuntu/ inflating: ShuTuUbuntu/ShuTu.Parameters.granule63XTest.dat inflating: ShuTuUbuntu/processImages.c inflating: ShuTuUbuntu/makefile inflating: ShuTuUbuntu/tinydir.h inflating: ShuTuUbuntu/ShuTu.Parameters.100X.dat inflating: ShuTuUbuntu/scaleSWC.c inflating: ShuTuUbuntu/ShuTu.Parameters.flyMotorNeuron.dat creating: ShuTuUbuntu/llist/ inflating: ShuTuUbuntu/llist/setup.py creating: ShuTuUbuntu/llist/src/ inflating: ShuTuUbuntu/llist/src/llist.c inflating: ShuTuUbuntu/llist/src/dllist.c inflating: ShuTuUbuntu/llist/src/py23macros.h inflating: ShuTuUbuntu/llist/src/sllist.c inflating: ShuTuUbuntu/llist/src/sllist.h 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inflating: ShuTuUbuntu/distro/lib/libasprintf.so.0.0.0 inflating: ShuTuUbuntu/distro/lib/libicutu.so inflating: ShuTuUbuntu/distro/lib/libiconv.la inflating: ShuTuUbuntu/distro/lib/libQtNetwork.la inflating: ShuTuUbuntu/distro/lib/libQtUiTools.a inflating: ShuTuUbuntu/distro/lib/libQtDBus.so inflating: ShuTuUbuntu/distro/lib/libfftw3l.la inflating: ShuTuUbuntu/distro/lib/libQtGui.so.4 inflating: ShuTuUbuntu/distro/lib/libfftw3l.so inflating: ShuTuUbuntu/distro/lib/libgcc_s.so.1 inflating: ShuTuUbuntu/distro/lib/libpcre.so.1.2.9 inflating: ShuTuUbuntu/distro/lib/libQtUiTools.prl inflating: ShuTuUbuntu/distro/lib/libgmodule-2.0.so.0.5104.0 inflating: ShuTuUbuntu/distro/lib/libfftw3f.so.3 creating: ShuTuUbuntu/distro/lib/girepository-1.0/ inflating: ShuTuUbuntu/distro/lib/girepository-1.0/PangoFT2-1.0.typelib inflating: ShuTuUbuntu/distro/lib/girepository-1.0/PangoCairo-1.0.typelib inflating: ShuTuUbuntu/distro/lib/girepository-1.0/Pango-1.0.typelib inflating: ShuTuUbuntu/distro/lib/girepository-1.0/HarfBuzz-0.0.typelib inflating: ShuTuUbuntu/distro/~.autosave.swc inflating: ShuTuUbuntu/distro/~20-22-1-10.autosave.swc creating: ShuTuUbuntu/distro/bin/ inflating: ShuTuUbuntu/distro/bin/config.xml creating: ShuTuUbuntu/distro/bin/doc/ inflating: ShuTuUbuntu/distro/bin/doc/index.html inflating: ShuTuUbuntu/distro/bin/doc/flyem_proofread_help.html inflating: ShuTuUbuntu/distro/bin/doc/ThirdPartyLibraries.txt inflating: ShuTuUbuntu/distro/bin/doc/menu.html inflating: ShuTuUbuntu/distro/bin/doc/shortcut.html inflating: ShuTuUbuntu/distro/bin/doc/shortcut_3d.html inflating: ShuTuUbuntu/distro/bin/ShuTu inflating: ShuTuUbuntu/ShuTuAutoTraceOneStack.c inflating: ShuTuUbuntu/analyzeSWC.py gcc -o generator generator.c ./generator <cdf.p >cdf.c gcc -c -fPIC cdf.c ./generator <fct.min.p >fct.min.c gcc -c -fPIC fct.min.c ./generator <filters.p >filters.c gcc -c -fPIC filters.c ./generator <linear.algebra.p >linear.algebra.c gcc -c -fPIC linear.algebra.c ./generator <array.p >array.c gcc -c -fPIC array.c ./generator <connectivity.p >connectivity.c gcc -c -fPIC connectivity.c ./generator <region.p >region.c gcc -c -fPIC region.c ./generator <fct.root.p >fct.root.c gcc -c -fPIC fct.root.c ./generator <image.p >image.c gcc -c -fPIC image.c ./generator <utilities.p >utilities.c gcc -c -fPIC utilities.c ./generator <snake.p >snake.c gcc -c -fPIC snake.c ./generator <hash.p >hash.c gcc -c -fPIC hash.c ./generator <level.set.p >level.set.c gcc -c -fPIC level.set.c ./generator <water.shed.p >water.shed.c gcc -c -fPIC water.shed.c ./generator <fft.p >fft.c gcc -c -fPIC fft.c ./generator <draw.p >draw.c gcc -c -fPIC draw.c ./generator <histogram.p >histogram.c gcc -c -fPIC histogram.c ./generator <swc.p >swc.c gcc -c -fPIC swc.c ./generator <paths.p >paths.c gcc -c -fPIC paths.c ./generator <mylib.p >mylib.c gcc -c -fPIC mylib.c ./generator <svg.p >svg.c gcc -c -fPIC svg.c cd MY_TIFF && make && cd .. make[1]: Entering directory '/content/ShuTuUbuntu/mylib/MY_TIFF' gcc -o generator generator.c ./generator <tiff.io.p >tiff.io.c gcc -c -fPIC tiff.io.c ./generator <tiff.image.p >tiff.image.c gcc -c -fPIC tiff.image.c ld -r -o mytiff.o tiff.io.o tiff.image.o ./generator <utilities.p >utilities.c gcc -c -fPIC utilities.c gcc -fPIC -o tiffconvert app.convert.c utilities.o mytiff.o gcc -fPIC -o tifftagger app.tagger.c utilities.o mytiff.o gcc -fPIC -o tiffRGB app.color.c utilities.o mytiff.o gcc -fPIC -o tiffshow app.show.c utilities.o mytiff.o gcc -fPIC -o mrc2tiff app.mrc2.c utilities.o mytiff.o make[1]: Leaving directory '/content/ShuTuUbuntu/mylib/MY_TIFF' cd MY_FFT && make && cd .. make[1]: Entering directory '/content/ShuTuUbuntu/mylib/MY_FFT' gcc -c -fPIC fft.F.c gcc -c -fPIC fft.D.c gcc -c -fPIC myfft.c make[1]: Leaving directory '/content/ShuTuUbuntu/mylib/MY_FFT' ar cr libmylib.a cdf.o fct.min.o filters.o linear.algebra.o array.o connectivity.o region.o fct.root.o image.o utilities.o snake.o hash.o level.set.o water.shed.o fft.o draw.o histogram.o swc.o paths.o mylib.o svg.o MY_FFT/myfft.o MY_TIFF/mytiff.o ranlib libmylib.a gcc -fPIC -c libShuTu.c -Imylib gcc -shared -o libShuTu.so libShuTu.o -Lmylib -lmylib -lm gcc -fPIC -c ShuTuAutoTraceOneStack.c -Imylib gcc -o ShuTuAutoTraceOneStack ShuTuAutoTraceOneStack.o libShuTu.o -Lmylib -lmylib -lm mpicc -fPIC -c ShuTuAutoTrace.c -Imylib mpicc -o ShuTuAutoTrace ShuTuAutoTrace.o libShuTu.o -Lmylib -lmylib -lm mpicc -fPIC -c createTiffStacksZeiss.c -Imylib mpicc -o createTiffStacksZeiss createTiffStacksZeiss.o libShuTu.o -Lmylib -lmylib -lm mpicc -fPIC -c processImages.c -Imylib mpicc -o processImages processImages.o libShuTu.o -Lmylib -lmylib -lm mpicc -fPIC -c stitchTiles.c -Imylib mpicc -o stitchTiles stitchTiles.o libShuTu.o -Lmylib -lmylib -lm mpicc -fPIC -c scaleSWC.c -Imylib mpicc -o scaleSWC scaleSWC.o libShuTu.o -Lmylib -lmylib -lm
Last line above here should eventually be:
mpicc -o scaleSWC scaleSWC.o libShuTu.o -Lmylib -lmylib -lm